What are the main COVID-19 variants? How can they affect vaccine responses?
24 February 2021. Related: COVID-19: vaccine research, COVID-19: transmission & prevention, COVID-19.
Simon Collins, HIV i-Base
Although all viruses change and evolve the new coronavirus variants are especially important because we now have effective vaccines.
By February 2021, several well-publicised variants have been described with brief characteristics listed in Table 1.
Although they were first reported in one country most were soon also reported in others. Some of these variants are transmitted more easily and some might affect how well vaccines work. This impact is still being studied but an early paper already reports a small but significant impact. [1]
Currently, the most serious is called B.1.351 (initially reported in South Africa).
However, all manufacturers are already testing updated versions of their vaccines against these new variants.
Variants are also categorised as variants of interest (VOI) when first identified. The become variants of concern (VOC) if they have characteristics that are associated with faster transmission or more serious clinical outcomes.
Table 1: Key variants and predicted impact on current vaccines
| Date reported | Original region | Name | Mutation | Impact | Comment |
| April 2020 | Western Europe (Italy, Germany) – but quickly global. | B.1 or D614G.1 (“Doug”) | D614G in the S-protein |
Quickly became main global strain. | Increased the replication efficiency and transmissibility. NAbs still recognised |
| June 2020 | Denmark | By November reported in more than 200 mink farms and in humans. >1.4 million animals culled. | 7 unique variants in S protein. | Mink-related outbreaks also reported in the Netherlands, Spain, Sweden, Italy and the US. | These are small and largely contained reports. No information on impact on vaccines. |
| August 2020. | UK (Kent) | B.1.1.7 (also 20I/501Y.V1 and VUI 202012/01 – variant under investigation) |
23 mutations including N501Y and others in S-protein. | Expanded in UK Nov to Jan. >600 cases reported in 33 US states. | Increased transmission. NAbs still recognised by Oxford, Pfizer and Moderna vaccines. Reduces sensitivity to neutralising Abs. |
| October 2020. | South Africa | B.1.351 (also 20H/501Y.V2) | 17 unique mutations in both S and N terminal including K417N, E484K and N501Y). | Already reported in 50 countries including the US. | E484K might cause some reduction in NAb but impact is not fully known. Reduced efficacy has been reported to Pfizer, Moderna, Oxford and Novavax vaccines. Reduces sensitivity to neutralising Abs. |
| November 2020. | New York | B.1.526. | Includes E484K. | Increased from 3% in Jan to ~40% of cases in NYC by April 2021. | So far: “does not lead to more severe disease” (MMWR report). |
| January 2021. | Brazil (but detected in travelers to Japan). | P.1 (also as 20J/501Y.V3) B.1.1.248 (variants of B.1.1.28). |
More sequence changes in both S and N terminal including K417N, E484K and N501Y). | Already reported in many countries including Japan, Brazil, Germany and the US. | Not yet known. |
| January 2021 (designated VOC in March). | California or Colorado. | CAL.20C B.1.427/ B.1.429 |
ORF1a: I4205V, ORF1b:D1183Y, S: S13I, W152C, L452R. | Increasing in California, 20% in Colorado by March, but so far limited to the US. | “Modest” increase in risk of transmission. Also MMWR report. |
| March 2021 | Tanzania | NK | Multiple new mutations reported. | Tanzania, few details. | Impact not yet known. |
| April 2021 | India | VOC-21APR-02
B.1.617.2 and two others B.1.617.1 and B.1.617.3. |
13 mutations, 7 in S-protein, including L452R and E484Q. | Detected in London, the US and 18 other countries (not currently in Africa). | “At least as transmittable as UK B.1.1.1.7”. Limited clinical data or impact on vaccines. |
References and further reading
Karim A et al. New SARS-CoV-2 Variants — Clinical, Public Health, and Vaccine Implications. N Engl J Med 2021; 384:1866-1868. DOI: 10.1056/NEJMc2100362. (13 May 2021).
https://www.nejm.org/doi/full/10.1056/NEJMc2100362
Wang Z et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. bioRxiv preprint. DOI:10.1101/2021.01.15.426911. (30 January 2021).
https://www.biorxiv.org/content/10.1101/2021.01.15.426911v2
A guide to emerging SARS-CoV-2 variants. The Scientist. (26 January 2021).
https://www.the-scientist.com/news-opinion/a-guide-to-emerging-sars-cov-2-variants-68387
Multitude of coronavirus variants found in the US — but the threat is unclear. Nature. (5 March 2021).
https://www.nature.com/articles/d41586-021-00564-4
WHO website on variants
https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/
The following websites include sophisticated databases including details genome sequencing. They also epidemiological maps of variant distribution and spread by country and more detail on naming and categorising variants.
https://covariants.org/variants
https://nextstrain.org/sars-cov-2
https://www.gisaid.org
This article was first posted on 10 February 2021. It has been updated several times as new information becomes available (last on 7 May 2021).
